YaqpOntEntity.java

/*
 *
 * YAQP - Yet Another QSAR Project:
 * Machine Learning algorithms designed for the prediction of toxicological
 * features of chemical compounds become available on the Web. Yaqp is developed
 * under OpenTox (http://opentox.org) which is an FP7-funded EU research project.
 * This project was developed at the Automatic Control Lab in the Chemical Engineering
 * School of National Technical University of Athens. Please read README for more
 * information.
 *
 * Copyright (C) 2009-2010 Pantelis Sopasakis & Charalampos Chomenides
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 *
 * Contact:
 * Pantelis Sopasakis
 * chvng@mail.ntua.gr
 * Address: Iroon Politechniou St. 9, Zografou, Athens Greece
 * tel. +30 210 7723236
 */
package org.opentox.ontology.namespaces;

import com.hp.hpl.jena.ontology.OntClass;
import com.hp.hpl.jena.rdf.model.Property;
import com.hp.hpl.jena.rdf.model.RDFNode;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.SimpleSelector;
import com.hp.hpl.jena.rdf.model.StmtIterator;
import com.hp.hpl.jena.rdf.model.impl.ResourceImpl;
import com.hp.hpl.jena.vocabulary.RDFS;
import java.io.Serializable;
import java.util.HashSet;
import java.util.Set;
import org.opentox.io.publishable.OntObject;
import org.opentox.io.publishable.RDFObject;
import org.opentox.ontology.interfaces.JOntEntity;

/**
 * Ontological Entity for YAQP. Ontological Entities include ontological classes
 * and properties. Example of such entities, are the OpenTox Algorithms, the OT Classes
 * and the OT Properties defined in the corresponding java classes.
 *
 * @author Pantelis Sopasakis
 * @author Charalampos Chomenides
 * @see JOntEntity interface for this class
 */
public class YaqpOntEntity implements JOntEntity, Serializable  {

    protected  static final String _NS_OT = "http://www.opentox.org/api/1.1#%s";
    protected  static final String _NS_AlgorithmTypes = "http://www.opentox.org/algorithmTypes.owl/#%s";
    public  static final String NS_OT_core = String.format(_NS_OT, "");
    public  static final String NS_AlgorithmTypes = String.format(_NS_AlgorithmTypes, "");

    protected static OntObject _model = new RDFObject();
    protected Resource _resource;

    public YaqpOntEntity() {
    }

    public YaqpOntEntity(Resource resource) {
        this._resource = resource;
    }

    /**
     * TODO: This is not tested yet!
     * @param resourceUri
     */
    public YaqpOntEntity(String resourceUri){
        this._resource = _model.createResource(resourceUri);
    }

    public OntClass createOntClass(OntObject model) {
        return model.createClass(getURI());
    }

    public Resource getResource() {
        return this._resource;
    }

    public OntClass getOntClass(OntObject model) {
        OntClass cl = model.getOntClass(getURI());
        if (cl==null){
            cl = createOntClass(model);
        }
        return cl;
    }

    public String getURI() {
        return _resource.getURI();
    }

    public Property createProperty(OntObject model) {
        return _model.createProperty(getURI());
    }

    public Set<Resource> getSuperEntities(){
        RDFObject tom = new RDFObject();
        tom.includeOntClass(this);
        StmtIterator stmtit = tom.listStatements(new SimpleSelector(null, RDFS.subClassOf, (RDFNode)null));
        Set<Resource> set = new HashSet<Resource>();
        while (stmtit.hasNext()){
            Resource superClass = stmtit.next().getObject().as(Resource.class);
            set.add(superClass);
        }
        return set;
    }
}